Selvatti Alexandre Pedro, Takezaki Naoko
Department of Zoology, Biology Institute, Rio de Janeiro State University - UERJ, Rio de Janeiro, Brazil.
Laboratory of Life Sciences, Faculty of Medicine, Kagawa University, Kagawa, Japan.
Front Bioinform. 2025 Aug 7;5:1563786. doi: 10.3389/fbinf.2025.1563786. eCollection 2025.
Palaeognathae is an ancient bird lineage that includes the volant tinamous and six flightless lineages: ostrich, rhea, cassowary, emu, kiwi (extant) and moa, elephant bird (extinct). Over the past decade, a consensus has emerged on the relationships within the group. In this consensus, the ostrich branch splits first, followed by rheas, a clade containing tinamou and moa and a clade with the emu and cassowary sister to the kiwi and elephant bird. However, the timing of the origin of these major clades remains uncertain. In phylogenomic studies, the origin of the crown Palaeognathae is typically dated to the K-Pg boundary (∼66 Ma), though one study suggested a younger Early Eocene age (∼51 Ma). This discrepancy might result from the number and position of fossil priors (calibration strategies) or by differences in genomic regions sampled (data types). We investigated the impact of calibration strategies and data types on the timing of the Palaeognathae root using genomic sequences from nuclear (noncoding [CNEE and UCE] and coding [first and second codon positions]) and mitogenomic datasets. The nuclear dataset included 14 Palaeognathae species (13 extant and the extinct moa), while the mitogenomic included 31 species, covering all extant and extinct lineages. The datasets were analyzed with and without internal calibrations. The age estimates were more influenced by calibration strategy than data type, although some nuclear data (CNEE) produced substantially younger ages except for the Casuariiformes node, whilst another dataset (PRM) from a previous study estimated younger ages for Casuariiformes compared to the other datasets. Nevertheless, our results consistently placed the origin of crown Palaeognathae around the K-Pg boundary (62-68 Ma), even when using the original dataset that produced the Eocene age. These findings demonstrate that multiple internal calibrations yield consistent results across different sequence types and taxon schemes, providing robust estimates of the crown Palaeognathae age. This improved timing enhances our understanding of the early evolutionary history of this clade, particularly regarding the placement of enigmatic Paleocene fossils, such as Lithornithidae and , which in this timeframe can be assigned to internal branches within the crown Palaeognathae.
古颚类是一个古老的鸟类谱系，包括会飞的䳍形目鸟类以及六个不会飞的谱系：鸵鸟、美洲鸵、食火鸡、鸸鹋、几维鸟（现存）和恐鸟、象鸟（已灭绝）。在过去十年里，该类群内部的关系已达成共识。在这个共识中，鸵鸟分支最先分化，接着是美洲鸵，一个包含䳍形目鸟类和恐鸟的分支，以及一个鸸鹋和食火鸡与几维鸟和象鸟为姐妹群的分支。然而，这些主要分支的起源时间仍然不确定。在系统基因组学研究中，冠古颚类的起源通常被定在白垩纪 - 古近纪界线（约6600万年前），尽管有一项研究提出了更晚的始新世早期年龄（约5100万年前）。这种差异可能是由于化石先验信息的数量和位置（校准策略），或者是由于所采样的基因组区域（数据类型）的差异。我们使用来自核基因组（非编码[保守非编码元件和超保守元件]和编码[第一和第二密码子位置]）和线粒体基因组数据集的基因组序列，研究了校准策略和数据类型对古颚类根部起源时间的影响。核基因组数据集包括14种古颚类物种（13种现存的和已灭绝的恐鸟），而线粒体基因组数据集包括31种物种，涵盖了所有现存和已灭绝的谱系。对数据集进行了有无内部校准的分析。年龄估计受校准策略的影响比数据类型更大，尽管一些核数据（保守非编码元件）除了食火鸡目节点外产生的年龄要小得多，而先前一项研究中的另一个数据集（PRM）与其他数据集相比，对食火鸡目估计的年龄更小。尽管如此，我们的结果始终将冠古颚类的起源置于白垩纪 - 古近纪界线附近（6200 - 6800万年前），即使使用产生始新世年龄的原始数据集。这些发现表明，多个内部校准在不同的序列类型和分类方案中产生一致的结果，为冠古颚类的年龄提供了可靠的估计。这个改进后的时间框架增强了我们对这个类群早期进化历史的理解，特别是关于神秘的古新世化石的位置，比如始祖鸟科，在这个时间范围内它们可以被归入冠古颚类的内部分支。
